XFM2DEF(1) MINC User's Guide XFM2DEF(1)NAME
xfm2def - convert a MNI transform file to a deformation volume
SYNOPSIS
xfm2def [options] input.xfm def_vol.mnc
DESCRIPTION
xfm2def takes an input transform input.xfm that can consist of a series of concatenated transforms in a single xfm file and converts this
into a single deformation volume that is output as def_vol.mnc. Note that the output is not a tranform file itself, you can then make use
of this volume in a MINC tranform by creating an .xfm file as such:
MNI Transform File
Transform_Type = Grid_Transform;
Displacement_Volume = def_vol.mnc;
The output resolution and sampling of the deformation grid must be specified or a default size will be used. (100x100x100 1mm steps centred
around the origin).
OPTIONS -help Print summary of command-line options and exit.
-version
Print the program's version number and exit.
-verbose
Print out extra progress information while running.
-clobber
Overwrite any existing output file
-xnelements nx
Number of elements along the xspace dimension.
-ynelements ny
Number of elements along the yspace dimension.
-znelements nz
Number of elements along the zspace dimension.
-xstep xstep
Step between voxels along the xspace dimension.
-ystep ystep
Step between voxels along the yspace dimension.
-zstep zstep
Step between voxels along the zspace dimension.
-xstart xstart
Position of centre of first voxel along the xspace dimension.
-ystart ystart
Position of centre of first voxel along the yspace dimension.
-zstart zstart
Position of centre of first voxel along the zspace dimension.
-xdircos x1 x2 x3
Direction cosines for the xspace dimension.
-ydircos y1 y2 y3
Direction cosines for the yspace dimension.
-zdircos z1 z2 z3
Direction cosines for the zspace dimension.
AUTHOR
Andrew Janke
COPYRIGHTS
Copyright (C) 2010 Andrew Janke - a.janke@gmail.com
$Date: 2010-08-11 04:06:42 $ XFM2DEF(1)
Check Out this Related Man Page
nii2mnc(1)nii2mnc(1)NAME
nii2mnc - convert a NIfTI-1 or Analyze 7.5 format file to a MINC format file.
SYNOPSIS
nii2mnc [<options>] <infile> <outfile.mnc>
nii2mnc -help
DESCRIPTION
The nii2mnc command is used to convert "NIfTI-1" format files to MINC format. The NIfTI-1 format was developed by the members of the Neu-
roinformatics Technology Initiative's Data Format Working Group (DFWG). The NIfTI-1 format is based upon the Mayo Clinic's Analyze 7.5
format.
The name of the program is derived from the common filename suffixes used for NIfTI-1 and MINC files. NIfTI-1 defines two possible for-
mats, a "header plus raw image" 2-file format, and a single-file format that includes both header information and the image data. As with
Analyze 7.5, the 2-file format consists of one file with the suffix ".hdr" and another file with the extension ".img". In NIfTI-1 single-
file format, the two files may be combined into a single file with a ".nii" filename suffix.
OPTIONS
Note that options can be specified in abbreviated form (as long as they are unique) and can be given anywhere on the command line.
Output voxel format-float Save voxels in 32-bit floating point format
-double
Save voxels in 64-bit floating point format
-byte Save voxels in 8-bit integer format
-short Save voxels in 16-bit integer format
-int Save voxels in 32-bit integer format
-signed
Save voxels in signed (2's complement) integer format
-unsigned
Save voxels in unsigned integer format
Analyze 7.5 specific options-transverse
Assume data is in ZYX dimension order.
-sagittal
Assume data is in XZY dimension order.
-coronal
Assume data is in YZX dimension order.
-xyz Assume data is in XYZ dimension order.
-zxy Assume data is in ZXY dimension order.
-yxz Assume data is in YXZ dimension order.
-flipx, -flipy, -flipz
Invert the samples along the given axis.
Other options-noscanrange
Don't scan data to determine valid range.
-quiet Quiet operation - do not print progress or debugging information.
Generic options for all commands-help Print summary of command-line options and abort
-version
Print the program and library versions and abort
KNOWN BUGS
Current handling of NIfTI-1 qform and sform coordinate transforms should probably be revised as the NIfTI group clarifies the correct usage
of these fields.
SEE ALSO
mnc2nii
AUTHOR
Robert Vincent (bert@bic.mni.mcgill.ca) with assistance from the NIfTI-1 library authored by Robert Cox et al.
COPYRIGHTS
Copyrights 2005 by Robert Vincent for the Montreal Neurological Institute.
$Revision: 1.4 $ Apr 22 2005 nii2mnc(1)